4.8 Article

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Related references

Note: Only part of the references are listed.
Article Plant Sciences

Optical topometry and machine learning to rapidly phenotype stomatal patterning traits for maize QTL mapping

Jiayang Xie et al.

Summary: This study presents a high-throughput epidermal cell phenotyping pipeline and QTL mapping in maize, demonstrating the genetic basis of stomatal patterning. Optical topometry and machine learning tools were used to assess epidermal cell patterning and analyze its genetic architecture alongside leaf photosynthetic gas exchange. Thirty-six consistent QTL and 24 clusters of overlapping QTL were identified, suggesting pleiotropy in multiple cases.

PLANT PHYSIOLOGY (2021)

Article Plant Sciences

Classical phenotyping and deep learning concur on genetic control of stomatal density and area in sorghum

Raju Bheemanahalli et al.

Summary: Through deep learning and genetic diversity characterization, the study identified significant genetic differences in stomatal traits in sorghum across different environments, revealing 71 genetic loci associated with stomatal traits and identifying putative causal genes underlying stomatal trait variation. This integrated physiological, deep learning, and genomic approach provides a foundation for further exploration of the genetic and molecular mechanisms controlling stomatal patterning and regulation in sorghum.

PLANT PHYSIOLOGY (2021)

Article Plant Sciences

Comparative evolutionary genetics of deleterious load in sorghum and maize

Roberto Lozano et al.

Summary: Comparative analysis of genomic variations between sorghum and maize revealed prevalent deleterious mutations in both species, particularly in pericentromeric regions, with sorghum showing a lower post-domestication genetic load compared to maize. This research provides insights into the evolutionary dynamics of deleterious variants in sorghum and offers a framework for prioritizing these variants for removal through genome editing and breeding.

NATURE PLANTS (2021)

Article Biochemistry & Molecular Biology

Agave angustifoliaalbino plantlets lose stomatal physiology function by changing the development of the stomatal complex due to a molecular disruption

Hernandez-Castellano Sara et al.

MOLECULAR GENETICS AND GENOMICS (2020)

Review Plant Sciences

Stomatal development in the grasses: lessons from models and crops (and crop models)

Katelyn H. McKown et al.

NEW PHYTOLOGIST (2020)

Article Multidisciplinary Sciences

HY5 is not integral to light mediated stomatal development in Arabidopsis

Nicholas Zoulias et al.

PLOS ONE (2020)

Article Genetics & Heredity

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum

Jhonathan P. R. dos Santos et al.

G3-GENES GENOMES GENETICS (2020)

Article Evolutionary Biology

Selection On synonymous Mutations Revealed by 1135 Genomes of Arabidopsis thaliana

Lai Wei

EVOLUTIONARY BIOINFORMATICS (2020)

Article Plant Sciences

Distinct branches of the N-end rule pathway modulate the plant immune response

Jorge Vicente et al.

NEW PHYTOLOGIST (2019)

Review Plant Sciences

Water-Use Efficiency: Advances and Challenges in a Changing Climate

Jerry L. Hatfield et al.

FRONTIERS IN PLANT SCIENCE (2019)

Review Plant Sciences

Impact of Stomatal Density and Morphology on Water-Use Efficiency in a Changing World

Ligia T. Bertolino et al.

FRONTIERS IN PLANT SCIENCE (2019)

Review Plant Sciences

Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C-3 and C-4 Crops

Andrew D. B. Leakey et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 70 (2019)

Article Plant Sciences

Reduced stomatal density in bread wheat leads to increased water-use efficiency

Jessica Dunn et al.

JOURNAL OF EXPERIMENTAL BOTANY (2019)

Article Genetics & Heredity

Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays

Karl A. G. Kremling et al.

G3-GENES GENOMES GENETICS (2019)

Article Multidisciplinary Sciences

Increased atmospheric vapor pressure deficit reduces global vegetation growth

Wenping Yuan et al.

SCIENCE ADVANCES (2019)

Article Biodiversity Conservation

Uncovering hidden genetic variation in photosynthesis of field-grown maize under ozone pollution

Nicole E. Choquette et al.

GLOBAL CHANGE BIOLOGY (2019)

Review Multidisciplinary Sciences

Genetic strategies for improving crop yields

Julia Bailey-Serres et al.

NATURE (2019)

Article Agronomy

Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum

Samuel B. Fernandes et al.

THEORETICAL AND APPLIED GENETICS (2018)

Article Biochemistry & Molecular Biology

Direct Control of SPEECHLESS by PIF4 in the High-Temperature Response of Stomatal Development

On Sun Lau et al.

CURRENT BIOLOGY (2018)

Article Multidisciplinary Sciences

Palisade cell shape affects the light-induced chloroplast movements and leaf photosynthesis

Eiji Gotoh et al.

SCIENTIFIC REPORTS (2018)

Article Plant Sciences

Genetic and Developmental Basis for Increased Leaf Thickness in the Arabidopsis Cvi Ecotype

Viktoriya Coneva et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Biochemistry & Molecular Biology

Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana

Hannes Dittberner et al.

MOLECULAR ECOLOGY (2018)

Article Agricultural Engineering

Performance evaluation of biomass sorghum in Hawaii and Texas

Manyowa N. Meki et al.

INDUSTRIAL CROPS AND PRODUCTS (2017)

Article Meteorology & Atmospheric Sciences

The Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA-2)

Ronald Gelaro et al.

JOURNAL OF CLIMATE (2017)

Article Plant Sciences

Genetic architecture of photosynthesis in Sorghum bicolor under non-stress and cold stress conditions

Diego Ortiz et al.

JOURNAL OF EXPERIMENTAL BOTANY (2017)

Article Biochemistry & Molecular Biology

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

Tian Tian et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Plant Sciences

Origins and Evolution of Stomatal Development

Caspar C. C. Chater et al.

PLANT PHYSIOLOGY (2017)

Article Multidisciplinary Sciences

Mobile MUTE specifies subsidiary cells to build physiologically improved grass stomata

Michael T. Raissig et al.

SCIENCE (2017)

Article Environmental Sciences

Root Water Uptake and Ideotypes of the Root System: Whole-Plant Controls Matter

Francois Tardieu et al.

VADOSE ZONE JOURNAL (2017)

Article Ecology

The anatomical and compositional basis of leaf mass per area

Grace P. John et al.

ECOLOGY LETTERS (2017)

Article Biotechnology & Applied Microbiology

PdEPF1 regulates water-use efficiency and drought tolerance by modulating stomatal density in poplar

Congpeng Wang et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

Article Energy & Fuels

QTL and Drought Effects on Leaf Physiology in Lowland Panicum virgatum

Samuel H. Taylor et al.

BIOENERGY RESEARCH (2016)

Article Plant Sciences

Mitogen activated protein kinase 4 (MPK4) influences growth in Populus tremula L. x tremuloides

Damian Witon et al.

ENVIRONMENTAL AND EXPERIMENTAL BOTANY (2016)

Review Plant Sciences

Expansins: roles in plant growth and potential applications in crop improvement

Prince Marowa et al.

PLANT CELL REPORTS (2016)

Article Multidisciplinary Sciences

Balancing Water Uptake and Loss through the Coordinated Regulation of Stomatal and Root Development

Christopher Hepworth et al.

PLOS ONE (2016)

Article Plant Sciences

Application of Optical Topometry to Analysis of the Plant Epidermis

Miranda J. Haus et al.

PLANT PHYSIOLOGY (2015)

Article Multidisciplinary Sciences

Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development

Cawas B. Engineer et al.

NATURE (2014)

Article Biochemical Research Methods

Efficient multivariate linear mixed model algorithms for genome-wide association studies

Xiang Zhou et al.

NATURE METHODS (2014)

Article Biochemistry & Molecular Biology

Insights into the Maize Pan-Genome and Pan-Transcriptome

Candice N. Hirsch et al.

PLANT CELL (2014)

Article Multidisciplinary Sciences

Variation in MPK12 affects water use efficiency in Arabidopsis and reveals a pleiotropic link between guard cell size and ABA response

David L. Des Marais et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Plant Sciences

Tradeoffs between functional strategies for resource-use and drought-survival in Mediterranean rangeland species

Ignacio M. Perez-Ramos et al.

ENVIRONMENTAL AND EXPERIMENTAL BOTANY (2013)

Article Plant Sciences

Drought induces alterations in the stomatal development program in Populus

Erin T. Hamanishi et al.

JOURNAL OF EXPERIMENTAL BOTANY (2012)

Article Genetics & Heredity

Genome-wide efficient mixed-model analysis for association studies

Xiang Zhou et al.

NATURE GENETICS (2012)

Article Genetics & Heredity

Shrinkage Estimation of the Realized Relationship Matrix

Jeffrey B. Endelman et al.

G3-GENES GENOMES GENETICS (2012)

Article Plant Sciences

Leaf Functional Anatomy in Relation to Photosynthesis

Ichiro Terashima et al.

PLANT PHYSIOLOGY (2011)

Review Plant Sciences

The iPlant collaborative: cyberinfrastructure for plant biology

Stephen A. Goff et al.

FRONTIERS IN PLANT SCIENCE (2011)

Review Plant Sciences

Environmental regulation of stomatal development

Stuart A. Casson et al.

CURRENT OPINION IN PLANT BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula

Par K. Ingvarsson

MOLECULAR BIOLOGY AND EVOLUTION (2010)

Article Agronomy

QTLs for early vigor of tropical maize

S. Trachsel et al.

MOLECULAR BREEDING (2010)

Article Biochemistry & Molecular Biology

PDS activity acts as a rheostat of retrograde signaling during early chloroplast biogenesis

Andrew Foudree et al.

PLANT SIGNALING & BEHAVIOR (2010)

Article Biochemistry & Molecular Biology

phytochrome B and PIF4 Regulate Stomatal Development in Response to Light Quantity

Stuart A. Casson et al.

CURRENT BIOLOGY (2009)

Article Multidisciplinary Sciences

The Sorghum bicolor genome and the diversification of grasses

Andrew H. Paterson et al.

NATURE (2009)

Article Biochemistry & Molecular Biology

Cryptochromes, Phytochromes, and COP1 Regulate Light-Controlled Stomatal Development in Arabidopsis

Chun-Ying Kang et al.

PLANT CELL (2009)

Article Multidisciplinary Sciences

Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time

Peter J. Franks et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Plant Sciences

CRR23/NdhL is a subunit of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis

Hideyuki Shimizu et al.

PLANT AND CELL PHYSIOLOGY (2008)

Review Plant Sciences

Status and Prospects of Association Mapping in Plants

Chengsong Zhu et al.

PLANT GENOME (2008)

Article Biochemical Research Methods

TASSEL: software for association mapping of complex traits in diverse samples

Peter J. Bradbury et al.

BIOINFORMATICS (2007)

Article Multidisciplinary Sciences

Termination of asymmetric cell division and differentiation of stomata

Lynn Jo Pillitteri et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Enemy at the Gates Interaction-Specific Stomatal Responses to Pathogenic Challenge

Elena Prats et al.

PLANT SIGNALING & BEHAVIOR (2007)

Article Biology

On the design of early generation variety trials with correlated data

B. R. Cullis et al.

JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS (2006)

Article Computer Science, Software Engineering

Distributed computing in practice: the Condor experience

D Thain et al.

CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE (2005)

Article Plant Sciences

Breeding for high water-use efficiency

AG Condon et al.

JOURNAL OF EXPERIMENTAL BOTANY (2004)

Review Multidisciplinary Sciences

The role of stomata in sensing and driving environmental change

AM Hetherington et al.

NATURE (2003)

Article Multidisciplinary Sciences

The structure of haplotype blocks in the human genome

SB Gabriel et al.

SCIENCE (2002)

Article Multidisciplinary Sciences

Plant development - Signals from mature to new leaves

JA Lake et al.

NATURE (2001)

Article Multidisciplinary Sciences

The HIC signalling pathway links CO2 perception to stomatal development

JE Gray et al.

NATURE (2000)